FOREST GENETICS DEDICATIONS To the people who have inspired and sustained me throughout my life: Mom, Dad, Mary, Dorothy, Suzie and Antonio. TW To Cathy, Christine, Michael, Patrick, Neal, Kenda, Halli, Jethro, Ashley, Lily and Clark. TA To my parents, Ken and Jane, who introduced me to the forests and trees of America. DN About the Cover This natural stand ofPinus tecunumanii is located in Las Piedrecitas, Chiapas, Mexico. This species occurs in a series of small disjunct populations from southern Mexico to cen- tral Nicaragua and was named for the famous Mayan chief "Tecun Uman." Pinus tecunu- manii is a cornerstone species in many forested ecosystems in Mesoamerica and is also established commercially in plantations outside of its natural range. The person climbing the tree is collecting seed as part of the ex situ gene conservation efforts for this species. (Photo courtesy of Dr. Bill Dvorak, Camcore, NCSU, Raleigh, NC, USA. Cover design by farm, Portland, Oregon). FOREST GENETICS TIMOTHY L. WHITE, Professor and Director, School of Forest Resources and Conservation, University of Florida W. THOMAS ADAMS, Professor and Head, Department of Forest Science, Oregon State University DAVID B. NEALE, Professor, Department of Plant Sciences, University of California, Davis www.cabi.org CABI Publishing is a division of CAB International CABI Publishing CABI Publishing CAB International 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: cabi@cabi.org E-mail: cabi-nao@cabi.org Website: www.cabi-publishing.org ©CAB International 2007. All rights reserved. No part of this publication may be repro- duced in any form or by any means, electronically, mechanically, by photocopying, re- cording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. A catalogue record for this book is available from the Library of Congress, Washington, DC. ISBN 9780851990835 The paper used for the text pages in this book is FSC certified. The FSC (Forest Steward- ship Council) is an international network to promote responsible management of the world's forests. Printed and bound in the UK from copy supplied by the editors by Cromwell Press, Trowbridge. CONTENTS IN BRIEF Chapter 1: Forest Genetics - Concepts, Scope, History and Importance 1 SECTION I: BASIC PRINCIPLES Chapter 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 15 Chapter 3: Transmission Genetics - Chromosomes, Recombination and Linkage 35 Chapter 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 53 Chapter 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 75 Chapter 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations 113 SECTIONII: GENETIC VARIATION IN NATURAL POPULATIONS Chapter 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 149 Chapter 8: Geographic Variation - Races, Clines andEcotypes 187 Chapter 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 231 Chapter 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies 259 SECTION III: TREE IMPROVEMENT Chapter 11: Tree Improvement Programs - Structure, Concepts and Importance 285 Chapter 12: Base Populations - Species, Hybrids, Seed Sources and Breeding Zones 303 Chapter 13: Phenotypic Mass Selection - Genetic Gain, Choice of Traits and Indirect Response 329 Chapter 14: Genetic Testing - Mating Designs, Field Designs and Test Implementation 357 Chapter 15: Data Analysis - Mixed Models, Variance Components and Breeding Values 395 Chapter 16: Deployment - Open-pollinated Varieties, Full-sib Families and Clones 439 Chapter 17: Advanced-generation Breeding Strategies - Breeding Population Size, Structure and Management 479 SECTION IV: BIOTECHNOLOGY Chapter 18: Genomics - Discovery and Functional Analysis of Genes 523 Chapter 19: Marker-assisted Selection and Breeding - Indirect Selection, Direct Selection and Breeding Applications 553 Chapter 20: Genetic Engineering - Target Traits, Transformation and Regeneration 573 v This page intentionally left blank CONTENTS Acknowledgments xvii Preface xix Chapter 1: Forest Genetics - Concepts, Scope, History and Importance 1 Global Scope and Importance of Natural and Managed Forests 1 The Role of Plantations as Forest Ecosystems 4 Concepts and Sources of Variation in Forests 6 Separating Genotypic and Environmental Influences on Phenotypic Variation 6 Environmental Sources of Variation 8 Genetic Sources of Variation 9 Historical Perspective onForest Genetics 11 General Genetics 11 Forest Genetics 13 Why Study Forest Genetics? 14 SECTION I: BASIC PRINCIPLES Chapter 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 15 Genome Organization 15 The DNA Molecule 15 Cellular Organization of Genomes 17 Genome Size 18 Chromosomes and Polyploidy 19 Karyotype Analysis 21 Repetitive DNA 22 Gene Structure and Regulation 26 The Central Dogma and the Genetic Code 26 Transcription and Translation 27 Structural Organization of a Gene 29 Regulation of Gene Expression 30 Summary and Conclusions 33 Chapter 3: Transmission Genetics - Chromosomes, Recombination and Linkage 35 Mendelian Genetics 35 Mendel's Crossing Experiments with Peas 35 Mendelian Inheritance of Traits in Forest Trees 38 Statistical Tests for Mendelian Inheritance 39 Transmission and Inheritance of Chromosomes 39 vii viii Contents Mitosis and Cell Division 40 Meiosis and Sexual Reproduction 42 Extensions to Mendel's Laws 45 Partial Dominance 45 Codominance 46 Epistasis 46 Genetic Linkage 47 Organelle Genome Inheritance 47 Summary and Conclusions 51 Chapter 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 53 Uses and Characteristics of Genetic Markers 53 Morphological Markers 54 Biochemical Markers 54 Monoterpenes 54 Allozymes 54 Other Protein Markers 55 Molecular Markers 55 DNA-DNA Hybridization: Restriction Fragment Length Polymorphism 57 Molecular Markers Based on the Polymerase Chain Reaction 64 Summary and Conclusions 74 Chapter 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 75 Quantifying the Genetic Composition of Populations 75 Genotype and Allele Frequencies 75 Hardy-Weinberg Principle 77 Mating Systems and Inbreeding 82 Influence of Inbreeding on Genotypic Frequencies 83 Inbreeding Coefficient and Regular Systems of Inbreeding 87 Inbreeding Depression 90 Forces that Change Allele Frequencies 94 Mutation 94 Migration 95 Selection 97 Genetic Drift 103 Joint Effects of Evolutionary Forces 107 Summary and Conclusions 109 Chapter 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations 113 The Nature and Study of Polygenic Traits 113 Characteristics of Polygenic Traits 113 Studying Polygenic Traits 115 Modeling Phenotypes of Parents and Offspring 117 Contents ix Clonal Value and Breeding Value 117 Estimating the Average Performance of Offspring 119 Genetic Variances and Heritabilities 123 Definitions and Concepts 123 Estimates of Heritabilities for Forest Trees 127 Uses and Importance of Heritability Estimates in Forest Tree Populations 128 Genetic Correlations 130 Definitions and Concepts 130 Trait-trait Correlations 132 Age-age Correlations 133 Genotype x Environment Interaction 134 Definitions and Concepts 134 Importance of G x E Interaction in Forest Trees 136 Estimating Genetic Parameters 140 Mating Design 141 Field Design 141 Study Implementation, Data Cleaning and Standardization 141 Data Analyses 143 Parameter Estimation and Interpretation 144 Summary and Conclusions 147 SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS Chapter 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 149 Quantifying Genetic Variation 149 Measures of Genetic Variation Based on Genetic Markers 150 Measures of Genetic Variation Based on Quantitative Traits 153 Genetic Diversity in Forest Trees 153 Estimates of Genetic Diversity from Genetic Markers 153 Estimates of Genetic Diversity from Quantitative Traits 158 Factors Promoting Genetic Diversity within Populations 158 Large Population Size 159 Longevity 162 High Levels of Outcrossing 162 Strong Migration between Populations 166 Balancing Selection 170 Mating System Dynamics in Forest Trees 173 Mechanisms Promoting High Levels of Outcrossing 173 Factors Leading to Unusually Low Levels of Outcrossing 174 Patterns of Cross-fertilization within Populations 177 Spatial and Temporal Genetic Structure within Populations 179 Spatial Genetic Structure 179 Temporal Genetic Structure 183 Practical Implications of Within-population Genetic Diversity 183 Genetic Improvements under Natural Regeneration Systems 183 Seed Collections in Natural Populations 184 x Contents Summary and Conclusions 185 Chapter 8: Geographic Variation - Races, Clines and Ecotypes 187 Definitions and Concepts Related to Geographic Variation 188 Provenances, Seed Sources and Races 188 Clines and Ecotypes 190 Varieties and Subspecies 192 Provenance x Environment Interaction 192 Experimental Methods Used to Study Geographic Variation 195 Genetic Markers for Studying Geographic Variation 196 Short-term Seedling Tests in Artificial Environments 198 Long-term Provenance Trials in Field Experiments 201 Patterns of Geographic Variation in Forest Trees 204 Racial Variation Associated with Environmental Differences 206 Racial Variation Not Associated with Environmental Differences 209 Species with Little or No Racial Variation 211 Geographic Patterns of Genetic Diversity 216 Implications of Geographic Variation for Seed Transfer 219 Setting Explicit Objectives of Provenance Selection 221 Lessons Learned from Previous Provenance Studies 222 A Decision Tree to Guide Seed Transfer Decisions 224 Types of Seed Transfer Guidelines and Logistics of Implementation 226 Summary and Conclusions 229 Chapter 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 231 Divergence, Speciation and Hybridization 231 Species Concepts 232 Mechanisms of Speciation 234 Hybridization and Introgression 236 Evolutionary History and Phytogeny 237 Evolutionary History 237 Phylogenetics 244 Molecular Mechanisms of Genome Evolution 254 Mutation and Nucleotide Diversity 254 Gene Duplication and Gene Families 254 Polyploidy 256 Coevolution 257 Pines and Rust Fungi 257 White Pines and Corvids 257 Summary and Conclusions 258 Chapter 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies 259 Threats to Genetic Diversity 260 Habitat Loss, Deforestation, and Fragmentation 260 Pathogens, Insects, Exotic Species and Movement of Genetic Material 261 [...]... of forest genetics in all types of forests ranging from pristine natural forests to monoculture plantations Therefore, this chapter begins with a brief discussion of the different types of forests in the world, and their scope and importance We then outline the causes of variation in forests, provide a brief history of forest genetics, and conclude with a discussion of the importance of forest genetics. .. meet global demands for forest products and also maintain valuable genetic resources The twenty-first century promises to be an exciting and productive period for all of genetics, including forest genetics WHY STUDY FOREST GENETICS? The primary reason to study forest genetics is to provide insight into the evolution, conservation, management and sustainability of the world's forests In more detail,... descent Forest genetics is the subdiscipline of genetics dealing with forest tree species In one sense forest trees are not model organisms for studying genetic principles because of their large size and long life spans However, the study of forest genetics is important precisely because of the unique biological nature of forest trees and also because of the social and economic importance of forests... resources, including forest products Thus, the most important reason to study forest genetics is to provide insight into the evolution, conservation, management and sustainability of the world's natural and managed forests For this reason, the intent of this book, Forest Genetics, is to describe concepts and applications of genetics in all types of forests ranging from pristine natural forests to monoculture... usage of common names Forest Genetics is intended for several audiences as: (1) A first course for advanced undergraduate and graduate students; (2) A reference for professionals working in forest genetics or forest management; (3) An introduction for forest scientists interested in other subdisciplines of forest genetics (e.g for quantitative geneticists interested in biotechnol- xix XX ogy or molecular... the same genotype (Photos courtesy of K Eldridge, CSIRO Australia, and T White, respectively) Knowledge of forest genetics is valuable for understanding the sustainability, conservation and management of all types of forests on the continuum shown in Fig 1.3 For 4 Forest Genetics example, deforestation is reducing the amount of forested land by nearly 1% annually in some countries (World Resources Institute,... CAB International 2007 Forest Genetics (T.W White, W.T Adams and D.B Neale) 1 2 Forest Genetics harvested is used for fuelwood and forests provide a range of indigenous uses (Fig l.la) However, in developed countries, 84% of harvested wood is used for industrial purposes (FAO, 1995a; Fig 1 Ib) In all countries, forests are valued for their conservation and scenic values While all forests provide many... environments Knowledge of general forest genetic principles and of genetic structure of forest tree species is required to develop sound gene conservation strategies Forest genetics can help us understand the implications and guide applications of silvicultural reforestation operations such as seed tree and shelterwood systems in forests managed with natural regeneration Forest genetics principles are central... engineering in forest trees To use this book as a first course in forest genetics, different chapters may be stressed, highlighted, or omitted completely, depending upon the orientation and objectives of the course A course in applied tree improvement might feature Chapters 1, 5-9 , and 1 1-1 7 with sections from other chapters highlighted as appropriate A course on genetics of natural forest populations... Tim White Gainesville, Florida tlwhite@ufl.edu Tom Adams Corvallis, Oregon w.t.adams@oregonstate.edu David Neale Davis, California dbneale@ucdavis.edu CHAPTER 1 FOREST GENETICS - CONCEPTS, SCOPE, HISTORY AND IMPORTANCE Genes are the basis for all genetic variation and biodiversity in the world, and genetics is the branch of biology that studies the nature, transmission and expression of genes Genetics . Perspective onForest Genetics 11 General Genetics 11 Forest Genetics 13 Why Study Forest Genetics? 14 SECTION I: BASIC PRINCIPLES Chapter 2: Molecular Basis of Inheritance - Genome. of this book, Forest Genetics, is to describe concepts and appli- cations of genetics in all types of forests ranging from pristine natural forests to monocul- ture plantations. The . of genetics is assumed. Forest Genetics is organized into four major sections. Section I, Chapters 2-6 , pro- vides a summary of basic genetic principles. Examples from forest